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Int. J. Mol. Sci. 2010, 11(10), 3725-3747; doi:10.3390/ijms11103725
Article

Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction

1,2,3
,
1,2
 and
1,2,3,4,*
1 Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA 2 Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA 3 Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA 4 Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
* Author to whom correspondence should be addressed.
Received: 3 September 2010 / Revised: 10 September 2010 / Accepted: 15 September 2010 / Published: 29 September 2010
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Abstract

Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding partners likely overlap the partner-sets of the originally identified MoRFs. The high abundance of MoRF-containing intrinsically disordered proteins in nature suggests the possibility that the number of retro-MoRFs could likewise be very high. This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level.
Keywords: reverse; retro; invert; alignment; intrinsic disorder; PONDR-RIBS reverse; retro; invert; alignment; intrinsic disorder; PONDR-RIBS
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).
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Xue, B.; Dunker, A.K.; Uversky, V.N. Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction. Int. J. Mol. Sci. 2010, 11, 3725-3747.

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